No extra deck

[Patroklos]

When I enter a match, the extra deck shows zero cards - on the deck constructer, the full 15 are present and correct.

Also, I cannot add cards to the side deck in the deck constructer.

[Auke1993]

I think you may have put your Extra Deck cards in your Side Deck by mistake.
Thinking your Extra Deck was your Side Deck made it impossible for any main deck cards to be added to it, as that cannot be done to the Extra Deck.